Download 5 years of your life …

or mine as it turns out. Found this via a link from Google Scholar. I was looking for the HMMer acceleration paper, specifically to see if it had been cited, and found my thesis.
The HPC connection has to do with the amount of simulation that went into the calculations. Way back in the good old days, 64 atom supercells took 1 week for 100 time steps on the machines we had (borrowed SGI R3000’s). Last time I ran the code, it took all of 11 seconds per time step on my old Opteron 246 machine.
Scary. I’ll go back to my abaqus now …

[chuckle] “condensation” [/chuckle]
Condensed matter physics somehow becomes condensation.